User: Johannes Rainer

gravatar for Johannes Rainer
Johannes Rainer1.3k
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@jotsetung
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3 years, 7 months ago
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j**************@eurac.edu

PhD, Bioinformatics Group, Institute for Biomedicine, Eurac Research, Bolzano, Italy

 

Posts by Johannes Rainer

<prev • 236 results • page 1 of 24 • next >
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Comment: C: ensembldb error/bug: Can't locate Bio/EnsEMBL/ApiVersion.pm in @INC | fetchTable
... I guess so. I've never done that but it should work. ...
written 13 days ago by Johannes Rainer1.3k
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Comment: C: ensembldb error/bug: Can't locate Bio/EnsEMBL/ApiVersion.pm in @INC | fetchTable
... I just checked the tx IDs in the ncrna and the cdna files and they are not overlapping. So both files contain a different set of genes/transcripts. ...
written 13 days ago by Johannes Rainer1.3k
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Comment: C: ensembldb error/bug: Can't locate Bio/EnsEMBL/ApiVersion.pm in @INC | fetchTable
... I would assume that most (if not all) ncRNAs are in the ncrna fasta file (e.g. homo_sapiens/ncrna/Homo_sapiens.GRCh38.ncrna.fa.gz). I've checked and all of the IDs in this file are present in the EnsDb (for Ensembl version 92). ...
written 13 days ago by Johannes Rainer1.3k
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Answer: A: Create Ensembl transcript to gene IDs table with R ensembldb package for tximpor
... Re question 1: To get an overview of all available EnsDb databases for mouse you use AnnotationHub, not ensembldb: > library(AnnotationHub) > ah <- AnnotationHub() snapshotDate(): 2018-04-30 > query(ah, "EnsDb.Mmusculus") AnnotationHub with 6 records # snapshotDate(): 2018-04-30 # $da ...
written 4 weeks ago by Johannes Rainer1.3k
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Comment: C: ensembldb error/bug: Can't locate Bio/EnsEMBL/ApiVersion.pm in @INC | fetchTable
... Both the EnsDb from the link above and the cdna fasta file are based on Ensembl release 92, so all transcripts from the cdna fasta file should be in the EnsDb. Note however that transcript IDs in EnsDb databases are without the transcript version (e.g. the ".1" in "ENST00001.1"). Did you use ignoreT ...
written 5 weeks ago by Johannes Rainer1.3k
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Answer: A: Metabolite identification package
... I guess you have already identified the chromatographic peaks/features with xcms, what you could do then is to use the CAMERA package to find adducts and isotopes in your data. Ultimately you will however have to look up the m/z of your peaks in a database (like hmdb (https://hmdb.ca)) to find possi ...
written 7 weeks ago by Johannes Rainer1.3k
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Comment: C: ensembldb error/bug: Can't locate Bio/EnsEMBL/ApiVersion.pm in @INC | fetchTable
... Just in case you want the quick and easy way out: you can download the human EnsDb package for Ensembl v92 from: https://www.dropbox.com/s/plne78gvnznwbl7/EnsDb.Hsapiens.v92_2.0.0.tar.gz?dl=0 ...
written 9 weeks ago by Johannes Rainer1.3k
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Comment: C: ensembldb error/bug: Can't locate Bio/EnsEMBL/ApiVersion.pm in @INC | fetchTable
... I'm installing the Ensembl core databases locally and it takes ~ 4-5 hours (depdends on the species, human takes quite a while). If you're querying the databases at Ensembl it might take even longer. ...
written 9 weeks ago by Johannes Rainer1.3k
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Answer: A: ensembldb error/bug: Can't locate Bio/EnsEMBL/ApiVersion.pm in @INC | fetchTable
... Hi Ramiro, +1 for trying to build an EnsDb on your own. This requires however (as detailed in the vignette) a local installation of the Ensembl Perl API (http://www.ensembl.org/info/docs/api/api_installation.html) along with perl version 5.18.0. The function uses the Ensembl Perl API to query the E ...
written 9 weeks ago by Johannes Rainer1.3k
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Comment: C: Using massifquant for peak detection of generic matrix data?
... I haven't tried that yet, sorry. ...
written 3 months ago by Johannes Rainer1.3k

Latest awards to Johannes Rainer

Teacher 11 months ago, created an answer with at least 3 up-votes. For A: How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
Appreciated 11 months ago, created a post with more than 5 votes. For A: How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
Appreciated 11 months ago, created a post with more than 5 votes. For A: makeTxDbFromBiomart Error: 1: Space required after the Public Identifier
Popular Question 11 months ago, created a question with more than 1,000 views. For Plot data from VCF using Gviz?
Popular Question 11 months ago, created a question with more than 1,000 views. For reactome.db: reactome IDs not mapped to pathway names
Guru 11 months ago, received more than 100 upvotes.
Voter 11 months ago, voted more than 100 times.
Scholar 11 months ago, created an answer that has been accepted. For A: Is it possible to annotated mitochondrial genes with ENSEMBL ids and Homo.sapien
Scholar 11 months ago, created an answer that has been accepted. For A: How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
Scholar 11 months ago, created an answer that has been accepted. For A: Programatically download correct genome wide annotation package for given organi
Scholar 11 months ago, created an answer that has been accepted. For A: Is it possible to get Ensembl gene descriptions with ensembldb?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Is it possible to annotated mitochondrial genes with ENSEMBL ids and Homo.sapien
Scholar 12 months ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Great Question 12 months ago, created a question with more than 5,000 views. For Problem with biomart's listMarts function
Student 13 months ago, asked a question with at least 3 up-votes. For Easy way to sort GRangesList by seqname/start position?
Student 14 months ago, asked a question with at least 3 up-votes. For Problem with biomart's listMarts function
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Problem running dexseq in parallel using BiocParallel
Scholar 14 months ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: biomaRt no longer works with proxy after upgrade
Scholar 2.1 years ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Scholar 2.1 years ago, created an answer that has been accepted. For A: biomaRt package problem
Scholar 2.1 years ago, created an answer that has been accepted. For A: biomaRt no longer works with proxy after upgrade
Scholar 2.1 years ago, created an answer that has been accepted. For A: ensembldb: ensDbFromGtf error with ensembl version 74
Scholar 2.1 years ago, created an answer that has been accepted. For A: Missing SYMBOL keytype in EnsDb.Hsapiens.v75
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: makeTxDbFromBiomart Error: 1: Space required after the Public Identifier

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